The present invention relates to a method for reducing recombination events between nucleic acids. It also relates to the use of this method in processes for preparing nucleic acids such as plasmids or viral vectors. The invention also relates to novel viral constructs.
Recombination between nucleic acids is a well known phenomenon of molecular biology. Recombination is a molecular mechanism by which novel combinations of genetic material are generated, which contribute to Darwinian evolution by providing a source of material for natural selection. Genetic recombination requiring strong sequence homology between the participating nucleic acids is generally referred to as homologous recombination. During homologous recombination events, an exchange of genetic information occurs between two regions of a nucleic acid, this exchange possibly being reciprocal (xe2x80x9ccrossing overxe2x80x9d) or nonreciprocal (conversion).
During meiosis, homologous recombination is responsible for the rearrangement of the genetic information and plays an important role in the correct segregation of the chromosomes. During mitosis, homologous recombination participates in DNA repair. It can introduce genomic rearrangements, such as deletions and duplications, when it involves dispersed homologous regions, or also contractions or expansions when it involves tandem repeat sequences.
The mechanism by which homologous recombination occurs has been partly elucidated. Thus, in bacteria, homologous recombination begins with a step which involves a single-stranded end (Holliday, 1964; Meselson, 1975). In eukaryotes, on the other hand, most results suggest a mechanism of double-strand break (DSB) (Szostak et al., 1983). DSBs appear to be at the origin of two principal mechanisms of homologous recombination: one conservative, according to which all the nucleic acid sequences participating in the recombination are present in the recombination products (Szostak et al.), the other nonconservative, during which certain sequences are lost. In mammalian somatic cells the majority of homologous recombination events by DSB appear to take place according to a nonconservative process (Lin et al., 1990, Jeong-Yu, 1992).
With the constant-development of biotechnology, an ever-increasing exploitation of DNA is being carried out: production of recombinant proteins, creation of transgenic animals, gene therapy and cellular therapy, etc. In these different domains, the occurrence of uncontrolled recombination events can constitute, in certain cases, a drawback.
Thus, during the production of recombinant proteins, recombination events in the expression plasmid (intramolecular recombination) can for example lead to the excision of the expression cassette for the transgene and thus to a loss of the expression. Recombination events can also be at the origin of the excision of an expression cassette which is stably integrated into the genome of a host producer cell and thus can induce a loss of stability.
Another example of adverse effects linked to the occurrence of homologous recombination events is liable to take place during the construction and production of vectors, in particular of viral vectors. Viral vectors (adenovirus, retrovirus, adeno-associated virus, herpes virus, etc.) constitute particularly efficient means for transferring nucleic acids into cells in vitro, ex vivo or in vivo. For constructing defective viral vectors the regions which are essential for the replication of the wild-type virus are generally deleted from the genome and replaced with the nucleic acid of interest. To produce and amplify these viruses it is therefore necessary to supply, in trans, the complementing functions (either in a plasmid, or in a form which is integrated into the genome of the producer cell, or via a helper virus). However, in certain cases, homologous recombination events occur between the defective viral genome and the complementing functions, which reconstitute replicating viral particles. Thus, the vectors derived from adenoviruses are generally produced in a complementing line (293 line or derivative) into which part of the adenovirus genome has been integrated. More specifically, the 293 line contains the left-hand end (about 11-12%) of the genome of the adenovirus serotype 5 (Ad5), comprising the left ITR, the encapsidation region and the E1 region, including E1a, E1b, and part of the regions encoding the protein pIX and IVa2. This line is capable of transcomplementing recombinant adenoviruses which are defective for the E1 region, i.e. lacking in all or part of the E1 region, which is required for replication. However, there exist zones of homology between the region of the adenovirus which is integrated into the genome of the line and the DNA of the recombinant virus whose production is desired. For this reason, various recombination events can take place during production, generating replicating viral particles, in particular adenoviruses of type E1+. As indicated in FIG. 1, it can be a single recombination event followed by a break of the chromosome (FIG. 1A), or a double recombination (FIG. 1B). These two types of modification lead to the replacement of the left-hand portion of the recombinant DNA, lacking in a functional E1 region, with the corresponding portion present in the cell""s genome, which carries a functional copy of the E1 region. Moreover, taking into account the high titres of recombinant vector produced by the 293 line, the probability of these recombination events taking place is high. In fact, it has been found that many batches of defective recombinant adenoviral vectors are contaminated with replicating viral particles.
The presence of replicating particles in the batches of virus constitutes a considerable drawback for applications for transferring genes in vitro or in vivo (risks of viral propagation and uncontrolled dissemination).
The same type of problematics exist for generating defective retroviruses. Thus, constructed defective retroviruses are generally deleted of the viral coding regions (gag, pol and env), which are provided in trans by the production line. Here again, for certain lines described, overlapping zones exist between the genome of the defective retrovirus and the complementing functions carried by the cells. It is the case in particular for the cells PA317, Psi2, etc. Homologous recombination events can therefore take place in these zones, generating replicating particles.
The present invention relates to a method for reducing the frequency of the recombination events between two given nucleic acids and thus for minimizing the impact of such events on a biological process.
More particularly, the present invention relates to a method for reducing the frequency of the homologous recombination events between two given nucleic acids or two regions of a nucleic acid. To reduce homologous recombination events, the prior art teaches various approaches which are all based on the same principle: replacing or deleting the regions of homology. Thus, certain plasmids which allow the expression of genes of interest carry regions which are homologous to the genome of the host cell. It can be, in particular, a promoter region, a marker gene or an origin of replication. To reduce the risks of recombination, it has hitherto been proposed to substitute these regions with others, which are nonhomologous (different promoter, etc.). Moreover, to limit the risks of recombination in the processes for producing viral vectors, it has been suggested to remove the sequences which are homologous between the complementing genes and the defective viral genome. Thus, patent application WO 97/00326 describes a cell line for producing adenovirus, designated PER, comprising a restricted unit of the adenoviral genome carrying the E1 region. With this line, the flanking sequences which are homologous to the genome of the defective virus are reduced, which makes it possible to limit the risks of homologous recombination between them. Similarly, application WO 95/11984 describes the construction of a recombinant adenovirus carrying a deletion of the E1 region which is extended to a portion of the pIX gene. In this case, it is no longer the complementing region which is modified (reduced), but the deletion carried in the defective genome, which is extended. The result is also a decrease in the risks of recombination, even if regions of homology remain.
However, while these approaches make it possible to reduce the risks of recombination between the cell and the viral genome, and thus the risks of producing batches of virus which are contaminated with replicating particles, they do not make it possible to eliminate them entirely, and/or require the as construction and thus the validation of novel cell lines, which is very laborious. Moreover, the substitution of regions with others is not necessarily satisfactory, in particular in terms of efficacy.
The present application describes a novel method for reducing inter- or intramolecular homologous recombination events. The invention also describes the application of this method to the production of defective viruses which are not contaminated with replicating particles. The invention also describes novel viral constructs, which can be amplified in the existing production lines which are the most efficient in terms of the titre, with greatly reduced risks of generating replicating particles.
The initial and important step of homologous recombination is the recognition between the two partner nucleic acids (intermolecular recombination) or between two regions of a nucleic acid (intramolecular recombination). This step is the result of a direct interaction between the two homologous regions. Homologous recombination between two nucleic acids is thus based on the existence of sequence identity or strong sequence homology between two regions of these nucleic acids and is generally dependent upon two factors: the degree of homology and the length of the homology (i.e. of the homologous regions carried by the nucleic acid or the two nucleic acids). Moreover, the frequency of homologous recombination can also be influenced by certain specific regions of the nucleic acids. Thus, it has been observed that certain regions are capable of recombining with a frequency which is higher than the average frequency. It has moreover been determined that these localized variations in frequency could be due to specific sequences such as CHI sites in E. coli or M26 sites in S. pombe (Gangloff et al., 1994).
Unlike the strategies proposed in the prior art, the method of the invention does not involve deletion of the zones of homology between the partner nucleic acids. The method of the invention is based, in an original way, on the modification of the sequence of at least one of the two partner nucleic acids of the recombination, in such a way as to reduce the homology which exists between these nucleic acids.
A first subject of the invention thus relates to a method for reducing the frequency of intra- or intermolecular homologous recombination events between nucleic acids, characterized in that the sequence of at least one of the partner nucleic acids of the recombination is degenerated in such a way as to reduce the homology with the other partner(s).
For the purposes of the invention, xe2x80x9creduction of the frequency of homologous recombination eventsxe2x80x9d between nucleic acids is taken to mean any lowering of the said frequency, relative to the frequency observed with the unmodified corresponding nucleic acids. This reduction can easily be measured by conventional tests known to persons skilled in the art (in particular by xe2x80x9cmarker rescuexe2x80x9d tests or by tests for generation of replicating viral particles). Advantageously, the term xe2x80x9creductionxe2x80x9d is understood as a significant drop in the frequency of homologous recombination, preferably of at least one logarithmic unit.
xe2x80x9cIntermolecular homologous recombinationxe2x80x9d is intended to mean a homologous recombination between two different nucleic acids (or between two regions of two different nucleic acids). xe2x80x9cIntramolecular homologous recombinationxe2x80x9d is intended to mean a homologous recombination between two regions of the same nucleic acid. Moreover, the partner nucleic acids of the homologous recombination can be extrachromosomal nucleic acids, chromosomal nucleic acids or a combination of the two (i.e. a chromosomal nucleic acid and an extrachromosomal nucleic acid). The extrachromosomal nucleic acids can be plasmids, vectors, episomes, viral genomes, etc.
The method of the invention is particularly suited to reducing the frequency of the intermolecular homologous recombination events between a chromosomal nucleic acid and an extrachromosomal nucleic acid.
The method of the invention generally involves the following steps:
(i) identification of the region(s) responsible for the homologous recombination
(ii) modification of this or these regions
(iii) verification of the sequence
(iv) synthesis of the modified sequence (referred to as syngen)
(v) replacement of the original sequence with the syngen
(i) The identification of the regions responsible for homologous recombination between nucleic acids is carried out by any known method. In particular, as soon as a recombination event is observed, the regions which are responsible therefor can be investigated by sequence analysis: investigation of homologous regions between the nucleic acids (intermolecular) or within the nucleic acid (intramolecular).
When the sequences involved in the recombination are identified, a region is defined, comprising all or part of these sequences, which is used for step (ii) below, i.e. the modification.
(ii) Modification of the Sequence
It is generally accepted that the homology must be very strong over a sufficiently long region for recombination event to take place at a significant frequency. In particular, the data from the literature suggest that a region of perfect homology at least equal to about 200 pb in length is required for the occurrence of such events. Indeed, even though recombination events can take place over shorter regions, their frequency is much lower and irregular. Moreover, over such a region whose homology is reduced by 19%, it appears that the frequency of recombination is reduced by a factor 1000 (Waldman and Liskay, 1987).
The sequence can be modified in various ways. As regards coding sequence, modifications can be introduced based on the degeneracy of the genetic code. In this way the sequence is disturbed, and thus the homology is reduced, but the expression product is the same.
The invention resides therefore, in particular, in a modification of the sequence in such a way as to prevent the pairing between the two homologous regions. The modification makes it possible to decrease the length and degree of homology between the two regions concerned.
Advantageously, in the method of the invention, the sequence of the nucleic acid is degenerated, in the region involved in the homologous recombination, in a proportion of 1 base pair at least every 20 base pairs. More preferably, it is degenerated in a proportion of 1 base pair at least every 10 base pairs.
According to one particular variant of the invention, the sequence is degenerated over all the possible positions.
The degeneracy of the sequence according to the invention is advantageously produced as a function of the codon use of the cell or organism in which the nucleic acid should be used. In the case of a viral vector whose production is carried out in a human cell line, it is particularly advantageous to degenerate the sequences by favouring the preferred codon use in humans when this choice is possible (see examples).
Moreover, further modifications can be introduced into the nucleic acid sequence. Thus, in the noncoding regions it is possible to reduce the size of certain elements (regulatory sequences for expression, promoters) or to modify these elements or to substitute certain other elements with heterologous regions.
According to one particular variant of the invention, and when the zone of homology stretches over several genes, it is possible to reduce the zone of homology, on the one hand by degenerating the sequence of one or more genes, and on the other hand by modifying the genomic position of certain genes present in the zone of homology, i.e. by positioning these genes in the adenoviral genome and in a genomic position other than their original position. The sequence of the genes whose genomic position is modified can also be degenerated. Preferably, only the sequence of the genes which are not moved is degenerated.
(iii) Verification of the Sequence
The verification is carried out by data-processing methods which make it possible to detect the presence of regulatory elements, secondary structures, etc., which are liable to interfere with the activity of the syngen. See examples.
(iv) Synthesis of the Syngen
The syngen can be synthesized by any technique known to persons skilled in the art, and particularly by using nucleic acid synthesizers.
(v) Replacement of the Original Sequence With the Syngen
The syngen, once synthesized, is then introduced into the nucleic acid as a replacement for the original sequence. This step can also be carried out according to conventional molecular biology techniques well known to persons skilled in the art.
One of the applications of the method of the invention resides in the production of vectors, in particular viral vectors, devoid of replication-competent viral particles (RCV). In this respect, the method of the invention is directed more particularly towards reducing the frequency of the homologous recombination events between a chromosomal nucleic acid encoding complementing functions for a defective virus, and an extrachromosomal nucleic acid comprising the genome of the said defective virus.
The virus concerned can be advantageously an adenovirus, a retrovirus, an adeno-associated virus (AAV) or alternatively a herpes virus. It is more preferably an adenovirus.
Thus, one particular embodiment of the invention consists of a method for reducing the frequency of the homologous recombination events between a chromosomal nucleic acid comprising the E1 region of an adenovirus genome, as well as a flanking region, and an extrachromosomal nucleic acid comprising a genome of an adenovirus which is defective for the E1 region.
Advantageously, in this particular method, the degenerate sequence according to the invention comprises the pIX gene of the genome of the adenovirus which is defective for the E1 region. Even more preferably, the degenerate sequence comprises the pIX and IVa2 genes of the genome of the adenovirus.
According to another embodiment, the degenerate sequence comprises the pIX gene of the genome of the adenovirus, and the sequence of the Iva2 gene is moved from its natural locus to the E4 region.
The method of the invention is particularly suited to producing recombinant adenoviruses which are defective for the E1 region, in the 293 cell line or in a derived cell line.
As indicated above, the 293 cell line contains in its genome the left-hand portion of the genome of the adenovirus comprising in particular the E1 region and a flanking region which is located downstream (3xe2x80x2) of the E1 region and which carries in particular the pIX gene and part of the IVa2 gene. It is precisely in this flanking region that homologous recombination events which generate replication-competent adenoviruses (RCAs) take place. For the purposes of the invention, xe2x80x9cderived cell linexe2x80x9d is intended to mean a cell line carrying the E1 region of the adenovirus and a flanking region liable to give rise to recombination with the defective virus. It can be a shorter region than that present in 293 (limited to pIX for example) or a longer region. A derived line can also be a line which is constructed from 293-line cells by introducing additional complementing sequences (such as E4).
In this respect, the invention also relates to a method for preparing defective recombinant adenovirus by introducing, into a cell of the 293 line or into a derived cell, the genome of the said defective recombinant adenovirus, characterized in that the said genome carries:
a deletion of the E1 region
a degeneracy in the pIX and/or IVa2 genes.
The invention in addition relates to any viral vector whose genome comprises at least one region whose sequence is degenerated. It can be in particular retroviruses (carrying degenerate sequences in the gag, pol and/or env genes), AAVs (carrying degenerate sequences in the rep and/or cap genes) or also adenoviruses.
It is advantageously adenoviruses whose genome carries a degenerate pIX gene. Preferably, the degenerate sequence of the pIX gene is the sequence SEQ ID NO:1 or the sequence SEQ ID NO:6. More preferably, the adenovirus in addition carries a modification of the genomic position of the Iva2 gene. This gene is advantageously positioned in the E4 region.
According to another embodiment, it is an adenovirus whose pIX and IVa2 genes are degenerate. Preferably, the natural sequence of the pIX gene is replaced with the sequence SEQ ID NO:1 or the sequence SEQ ID NO:6 and the degenerate sequence of the IVa2 gene is the sequence SEQ ID NO:2 or the sequence SEQ ID NO:8. Preferably, the natural sequence of the pIX and IVa2 genes is replaced with the sequence SEQ ID NO:5.
According to another embodiment, it is an adenovirus whose pIX and IVa2 genes are degenerate and which in addition comprises modifications of the promoter sequence of the pIX gene and/or replacement of the polyadenylation sequence of these genes. Preferably, it is an adenovirus comprising the sequence SEQ ID NO:12.
The adenovirus in addition carries advantageously at least one deletion of the E1 region. More preferably, the adenoviruses are defective for all or part of the E1 and E3 regions at least. It can also be recombinant adenoviruses which are partially or totally defective for the E1 and E4 regions, and optionally for the E3 region. Moreover, this adenovirus can be of various serotypes. As far as the adenoviruses of human origin are concerned, mention may be made preferably of those classified in group C.
Even more preferably, among the various serotypes of human adenovirus, in the context of the present invention the adenoviruses of type 2 or 5 (Ad 2 or Ad 5) are preferred. Among the various adenoviruses of animal origin, in the context of the invention adenoviruses of canine origin are preferably used, and in particular all the strains of the CAV2 adenoviruses [Manhattan strain or A26/61 strain (ATCC VR-800) for example]. Other adenoviruses of animal origin are cited in particular in application WO 94/26914 incorporated herein by way of reference. The strategies for constructing adenoviruses, as well as the sites which can be used for introducing genes of interest into these vectors are described in detail in the prior art, and in particular WO 95/02697, WO 96/10088, WO 96/13596 or WO 96/22378.
According to one particularly advantageous embodiment, in the recombinant adenoviruses of the present invention the E1 region is inactivated by deletion of a PvuII-BglII fragment running from nucleotide 454 to nucleotide 3328 in the sequence of the Ad5 adenovirus. This sequence can be accessed in the literature and also on database (see in particular Genebank No. M73260). In another preferred embodiment, the E1 region is inactivated by deletion of a HinfII-Sau3A fragment running from nucleotide 382 to nucleotide 3446.
Advantageously, the recombinant adenoviruses of the invention in addition comprise a heterologous sequence of nucleic acids whose transfer and/or expression in a cell, an organ or an organism is desired.
In particular, the heterologous DNA sequence can comprise one or more therapeutic genes and/or one or more genes encoding antigenic peptides.
The therapeutic genes which can thus be transferred are any gene whose transcription and possibly translation in the target cell generate products having a therapeutic effect.
They can be, in particular, genes encoding protein products having a therapeutic effect. The protein product thus encoded can be a protein, a peptide, an amino acid, etc. This protein product can be homologous with respect to the target cell (i.e. a product which is normally expressed in the target cell when this cell has no pathological condition). In this case, the expression of a protein makes it possible for example to offset an insufficient expression in the cell or the expression of a protein which is inactive or weakly active because of a modification, or alternatively to overexpress the said protein. The therapeutic gene can also encode a mutant of a cellular protein, which has increased stability, modified activity, etc. The protein product can also be heterologous with respect to the target cell. In this case, an expressed protein can for example complement or provide an activity which is deficient in the cell, allowing it to combat a pathological condition.
Among the therapeutic products for the purposes of the invention, mention may be made more particularly of enzymes, blood derivatives, hormones, lymphokines: interleukins, interferons, TNFs, etc. (FR 9203120), growth factors, neurotransmitters or precursors thereof or synthesis enzymes, trophic factors: BDNF, CNTF, NGF, IGF, GMF, VEGF, aFGF, bFGF, NT3, NT5, etc.; apolipoproteins: ApoAI, ApoAIV, ApoE, etc. (FR 93 05125), dystrophin or a minidystrophin (FR 9111947), tumour suppresser genes; p53, Rb, Rap1A, DCC, k-rev, etc. (FR 93 04745), the genes encoding factors which are involved in clotting; Factors VII, VIII, IX, etc., the gene encoding the protein GAX, suicide genes: thymidine kinase, cytosine deaminase, etc., genes encoding single-chain (scFv) antibodies.
The therapeutic gene can also be a gene or an antisense sequence, whose expression in the target cell makes it possible to control the expression of genes or the transcription of cellular mRNAs. Such sequences can, for example, be transcribed in the target cell into RNAs which are complementary for cellular mRNAs, and can thus block their translation into protein, according to the technique described in patent EP 140 308.
As indicated above, the heterologous DNA sequence can also comprise one or more genes encoding an antigenic peptide which is capable of generating an immune response in humans. In this particular embodiment, the invention thus allows the production of vaccines which make it possible to immunize humans, in particular against microorganisms or viruses. They can be in particular antigenic peptides specific for the Epstein-Barr virus, the HIV virus, the hepatitis B virus (EP 185 573), the pseudo-rabies virus, or alternatively specific for tumours (EP 259 212).
Generally, the heterologous nucleic acid sequence also comprises a promoter region for functional transcription in the infected cell. It can be a promoter region which is responsible naturally for the expression of the gene under consideration when this region is capable of functioning in the infected cell. It can also be regions of different origin (which are responsible for the expression of other proteins, or are even synthetic). In particular, it can be promoter sequences of eukaryotic or viral genes. For example, it can be promoter sequences derived from the genome of the cell whose infection is desired. Similarly, it can be promoter sequences derived from the genome of a virus, including the adenovirus used. In this respect, mention may be made for example of the promoters of the E1A, MLP, CMV, RSV, etc. genes. In addition, these promoter regions can be modified by addition of sequences for activation or regulation, or which allow tissue-specific or tissue-predominant expression. Moreover, when the heterologous nucleic acid does not comprise promoter sequences, it can be inserted into the genome of the defective virus downstream of such a sequence.
Moreover, the heterologous nucleic acid sequence can also comprise, in particular upstream of the therapeutic gene, a signal sequence which directs the synthesized therapeutic product in the secretory pathways of the target cell. This signal sequence can be the natural signal sequence of the therapeutic product, but it can also be any other functional signal sequence or an artificial signal sequence.
Still in a particularly advantageous embodiment, the vectors of the invention in addition possess a functional E3 gene under the control of a heterologous promoter. More preferably, the vectors possess a portion of the E3 gene which allows the expression of the protein gp19K. This protein in fact makes it possible to avoid the adenovirus vector being the object of an immune reaction which (i) would limit its action and (ii) might have adverse side effects.
These recombinant vectors can be used for transferring nucleic acids into cells in vitro, ex vivo or in vivo.
The present invention also relates to any pharmaceutical composition comprising one or more recombinant adenovirus as described above. The pharmaceutical compositions of the invention can be formulated with a view to administration by topical, oral, parental, intranasal, intravenous, intramuscular, subcutaneous, intraocular, transdermal, etc. route.
Preferably, the pharmaceutical composition contains pharmaceutically acceptable vehicles for an injectable formulation. It can be in particular isotonic, sterile saline solutions (monosodium phosphate, disodium phosphate, sodium chloride, potassium chloride, calcium chloride or magnesium chloride, etc., or mixtures of such salts) or dry compositions, in particular lyophilized compositions, which by addition of sterilized water or physiological saline, depending on the case in question, allow injectable solutions to be made up.
The doses of virus used for the injection can be adapted as a function of various parameters, and in particular as a function of the method of administration used, the pathology concerned, the gene to be expressed, or alternatively the desired duration of the treatment. Generally, the recombinant adenoviruses according to the invention are formulated and administered in the form of doses between 104 and 1014 pfu/ml, and preferably 106 to 1010 pfu/ml. The term pfu (xe2x80x9cplaque-forming unitxe2x80x9d) corresponds to the infectious power of a viral solution, and is determined by infecting an appropriate cell culture and measuring, generally after 5 days, the number of plaques of infected cells. The techniques for determining the pfu titre of a viral solution are well documented in the literature.
The present invention will be described in greater detail with the aid of the following examples, which should be considered as illustrative and non-limiting.